Dear Amber experts,
Following my previous queries regarding adaptive solvent QM/MM dynamics, I focussed on one system only to narrow down the issues encountered while attempting to run this sort of simulations.
For comparison purposes with a previous study, I’m working with the system consisting in a protein-ligand complex to which a loop of another protein is docked and kept in this position by restraints applied to its borders. A Mg2+ ion is also present in the active site and I wish to treat quantum mechanically water molecules in the vicinity of the ligand (GTP). To do so, this is the input file I used:
Constant Temp 300K adQM/MD simulation
&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=50000, dt=0.001,
ntpr=10, ntwx=10, ntwr=100, ioutfm=1,
ntc=2, ntf=2,
noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,2828-2851,2941-2946',
ntr=1,
restraintmask = ':170,185,.CA,C,N',
restraint_wt=5.0,
ifqnt=1,
/
&qmmm
qmmask=':12,13,32,35,59,61,168,169,179,196-197',
qmcharge=-1,
adjust_q=0,
qm_theory='PM3',
qmshake=0,
qmcut=8.0,
vsolv=3,
writepdb=1,
/
&vsolv
nearest_qm_solvent_resname='WAT',
nearest_qm_solvent=2,
nearest_qm_solvent_fq=1,
nearest_qm_solvent_center_id=0,
qm_center_atom_id=2647,
/
&adqmmm
n_partition=4,
RA=7,
RT=9,
print_qm_coords=1,
/
As, before, I was getting the following error message:
> SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)
> Radius of QM region is smaller than the first partition.
> Reduce the number of solvent molecules in the active region or increase RA
I have increased the values of RA and RT from 5 and 7A to 7 and 9A, respectively. This enabled the simulation to begin.
Now, from the 4 partitions that result in mdout files 000, 001, 002 and 003, mdcrd and restrt files are created for the first one (000) only. Is this behaviour normal?
Then, the simulation is stopped due to the fourth partition which mdout file displays the following error message:
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
Yet, when checking the size of the QM region through the .pdb files written thanks to the “writepdb” keyword, this region doesn’t ‘blow up’ (see attachments named qmmm_region.pdb.*). Nevertheless, when checking this same region through the .xyz files generated thanks to the “print_qm_coords” keyword (QM_coords.* files), a residue from the loop of the second protein appears to be far away, as when visualising a wrapped trajectory that hasn’t been unwrapped. Moreover, in the .xyz file corresponding to the partition that leads to the halt of the simulation (QM_coords.003.xyz <
http://qm_coords.xyz/>), a water molecule is observed with the “wrapped” residue from the second protein such that this water molecule appears in both sides i.e. on the side of the protein-ligand complex and on the side of the second protein loop. Hence, I suspect this water molecule on “both sides” could be leading to the repeated "vlimit exceeded” messages I get:
vlimit exceeded for step 156; vmax = 20.4418
wrapping first mol.: -45.29463 -64.05628 0.00000
vlimit exceeded for step 157; vmax = 20.3292
wrapping first mol.: -45.54621 -64.41207 0.00000
vlimit exceeded for step 158; vmax = 20.2651
wrapping first mol.: -45.75854 -64.71234 0.00000
Could this be the case?
Any thoughts on what shall be done to pursue this adQM/MM simulation?
Thanking you in advance for any insights on this matter,
Sincerely,
Ruth
P.S: I’m running on a cluster with Amber 16
> On 15 May 2019, at 12:57, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>
> Dear Amber experts,
>
> I’m trying to run adaptive solvent QM/MM dynamics of a protein ligand complex containing a Mg2+ ion in the reactive region and that is treated quantum mechanically.
>
> I wish water molecules within 5A of an atom from the QM region (atom 2647) to be treated quantum mechanically during the run, so I set RA=5. As from previous calculations I have estimated that “exchange” happens between this distance and 7A, I have set RT=7.
>
> Now, while running these simulations with the following input:
>
> Constant Temp 300K adQM/MD simulation
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ntb=2, pres0=1.0, ntp=1, taup=1.0,
> cut=12.0,
> temp0=300.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> nstlim=50000, dt=0.001,
> ntpr=250, ntwx=200, ntwr=500, ioutfm=1,
> ntc=2, ntf=2,
> noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,2828-2851',
> ntr=1,
> restraintmask = ':170,185,.CA,C,N',
> restraint_wt=5.0,
> ifqnt=1,
> /
> &qmmm
> qmmask=':12,13,32,35,59,61,168,169,179',
> qmcharge=-1,
> adjust_q=1,
> qm_theory='PM3',
> qmshake=0,
> qmcut=8.0,
> vsolv=3,
> /
> &vsolv
> nearest_qm_solvent_resname='WAT',
> nearest_qm_solvent=4,
> nearest_qm_solvent_fq=1,
> nearest_qm_solvent_center_id=0,
> qm_center_atom_id=2647,
> /
> &adqmmm
> n_partition=8,
> RA=5,
> RT=7,
> print_qm_coords=1,
> /
>
>
> I get the following error message:
>
> SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)
> Radius of QM region is smaller than the first partition.
> Reduce the number of solvent molecules in the active region or increase RA
>
> But for an other system, using the following input (same values for RA, RT as you may see because the reaction center is absolutely identical):
>
> Constant Temp 300K adQM/MD simulation
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ntb=2, pres0=1.0, ntp=1, taup=1.0,
> cut=12.0,
> temp0=300.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> nstlim=50000, dt=0.001,
> ntpr=250, ntwx=200, ntwr=500, ioutfm=1,
> ntc=2, ntf=2,
> noshakemask = '.176-189,474-494,521-534,900-909,917-933,2646-2689,3859-3882',
> ifqnt=1,
> /
> &qmmm
> qmmask=':12,13,32,35,59,61,168,169,241',
> qmcharge=-1,
> adjust_q=1,
> qm_theory='PM3',
> qmshake=0,
> qmcut=8.0,
> vsolv=3,
> /
> &vsolv
> nearest_qm_solvent_resname='WAT',
> nearest_qm_solvent=5,
> nearest_qm_solvent_fq=1,
> nearest_qm_solvent_center_id=0,
> qm_center_atom_id=2647,
> /
> &adqmmm
> n_partition=8,
> RA=5,
> RT=7,
> print_qm_coords=1,
> /
>
> I get the following error message:
>
> SANDER BOMB in subroutine adaptive_qmmm (qmmm_adaptive_module)
> Radius of T region is larger than the biggest partition.
> Increase the number of partitions or reduce RT.
>
> So I wonder, how should I set RA and RT values (and the number of partitions as well) so that water molecules within 5A of the desired atom (2647) are treated quantum mechanically and their nature becomes MM at distances of 7A from this same atom?
>
> Thank you in advance for any insight into this matter.
>
> Sincerely yours,
>
> Ruth
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Received on Wed Jul 10 2019 - 04:00:02 PDT
